Human vs Red fox LastZ results
Human (Homo sapiens, GRCh38) and Red fox (Vulpes vulpes, VulVul2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 95. Human was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.
Configuration parameters
| Parameter | Value |
|---|---|
| Gap open penalty (O) | 400 |
| Gap extend penalty (E) | 30 |
| HSP threshold (K) | 3000 |
| Threshold for gapped extension (L) | 3000 |
| Threshold for alignments between gapped alignment blocks (H) | 2200 |
| Seed and Transition value (T) | 1 |
| Scoring matrix (Q) | Default:
A C G T
91 -114 -31 -123
-114 100 -125 -31
-31 -125 100 -114
-123 -31 -114 91
|
Chunking parameters
| Parameter | Human | Red fox |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 2,261,760 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 1,503,413,069 out of 3,099,750,718 |
Uncovered: 1,649,738 out of 38,571,754 |
| Red fox |
Uncovered: 924,476,602 out of 2,421,551,259 |
Uncovered: 1,804,128 out of 33,405,269 |
Block size distribution
| Size range | All 2,261,760 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 83,200 |
553.5 kb |
|||
| 10 bp - 100 bp | 274,168 |
13.0 Mb |
18,330 |
1.2 Mb |
|
| 100 bp - 1 kb | 1,352,382 |
609.5 Mb |
58,893 |
21.6 Mb |
|
| 1 kb - 10 kb | 551,402 |
1.0 Gb |
20,624 |
50.7 Mb |
|
| 10 kb - 100 kb | 601 |
8.4 Mb |
1,647 |
41.3 Mb |
|
| 100 kb - 1 Mb | 7 |
832.7 kb |
259 |
95.6 Mb |
|
| 1 Mb - 10 Mb | 269 |
991.2 Mb |
|||
| 10 Mb - 100 Mb | 33 |
480.6 Mb |
|||